New Zealand's top transport official has been accused of "acting unacceptably" after threatening to pull Wellington's transport funding.

During the New Zealand Transport Agency's select committee review this morning, Labour MP Phil Twyford grilled chief executive Geoff Dangerfield for threatening to pull transport funding for Wellington after the city council's opposition to the $90m flyover project.

"Do you think it's acceptable for an unelected public servant to make that judgement and threaten the democratically elect Wellington City Council?" Twyford asked.

Dangerfield was saved from answering by National MP, and committee chair, David Bennett, who rule the question out.

Twyford replied that he believed Dangerfield's behaviour was unacceptable.

In December last year, Wellington City Council voted to reneged on support for the flyover next to the iconic Basin Reserve cricket ground, voting instead to fund a $50,000 study looking at other options.

Supporters of further investigations said they believed the flyover would be an eyesore and further work was needed on a better solution to traffic congestion.

Dangerfield responded with a letter warning the council that its opposition could lead to funding cuts for other Wellington transport projects, including Public Transport Spine Study.

Asked this morning why he had threatened the council, Dangerfield said the spine study was linked to Basin Flyover and would be compromised if the flyover did not proceed.

He repeated that the flyover was the only viable way to ease congestion and all other options were either ineffective or unaffordable.